2P26

Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YUKPDB ENTRY 1YUK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62910.2M Magnesium acetate, 0.1M sodium acetate, pH4.6, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.8934.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.489α = 90
b = 30.853β = 94.29
c = 65.157γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2006-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7527.8721822

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YUK1.7527.8721815111791.340.2070.2040.253RANDOM20.372
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.210.2-0.020.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.744
r_dihedral_angle_3_deg15.033
r_dihedral_angle_4_deg12.783
r_dihedral_angle_1_deg5.817
r_scangle_it1.794
r_angle_refined_deg1.169
r_scbond_it1.101
r_mcangle_it0.649
r_mcbond_it0.378
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.744
r_dihedral_angle_3_deg15.033
r_dihedral_angle_4_deg12.783
r_dihedral_angle_1_deg5.817
r_scangle_it1.794
r_angle_refined_deg1.169
r_scbond_it1.101
r_mcangle_it0.649
r_mcbond_it0.378
r_nbtor_refined0.301
r_nbd_refined0.189
r_symmetry_vdw_refined0.185
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.111
r_chiral_restr0.08
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2156
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms42

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling